def parse_genofile(config, config_dic):
genofile = open(config_dic['genofile'], 'r')
meta_dic = {}
for line in genofile:
line = line.strip()
if len(line) == 0:
continue
if line.startswith('#'):
continue
if line.startswith('@'):
line = line.strip('@')
items = line.split(';')
for item in items:
kv = re.split(':|=', item)
meta_dic[kv[0].strip()] = kv[1].strip()
continue
if line.lower().startswith("chr"):
#
print("geno file meta dictionary:")
for k, v in meta_dic.items():
print("\t%s: %s" % (k, v))
#
print("geno file head:\n\t%s" % line)
strainnames = line.split()[4:]
config_dic['strains'] = datastructure.get_strains_bynames(inbredsetid=config_dic['inbredsetid'], strainnames=strainnames, updatestrainxref="yes")
continue
# geno file line, marker
marker_dic = parse_marker(line)
marker_dic['genoid'] = check_or_insert_geno(config_dic, marker_dic)
if check_genoxref(config_dic, marker_dic):
continue
insert_genodata(config, config_dic, marker_dic)
insert_genoxref(config_dic, marker_dic)
config_dic['dataid'] += 1
genofile.close()
def parse_genofile(config, config_dic):
genofile = open(config_dic['genofile'], 'r')
meta_dic = {}
for line in genofile:
line = line.strip()
if len(line) == 0:
continue
if line.startswith('#'):
continue
if line.startswith('@'):
line = line.strip('@')
items = line.split(';')
for item in items:
kv = re.split(':|=', item)
meta_dic[kv[0].strip()] = kv[1].strip()
continue
if line.lower().startswith("chr"):
#
print("geno file meta dictionary:")
for k, v in meta_dic.items():
print("\t%s: %s" % (k, v))
#
print("geno file head:\n\t%s" % line)
strainnames = line.split()[4:]
config_dic['strains'] = datastructure.get_strains_bynames(inbredsetid=config_dic['inbredsetid'], strainnames=strainnames, updatestrainxref="yes")
continue
# geno file line, marker
marker_dic = parse_marker(line)
marker_dic['genoid'] = check_or_insert_geno(config_dic, marker_dic)
if check_genoxref(config_dic, marker_dic):
continue
insert_genodata(config, config_dic, marker_dic)
insert_genoxref(config_dic, marker_dic)
config_dic['dataid'] += 1
genofile.close()
def main(argv):
# config
config = utilities.get_config(argv[1])
print "config:"
for item in config.items('config'):
print "\t%s" % (str(item))
# var
inbredsetid = config.get('config', 'inbredsetid')
print "inbredsetid: %s" % inbredsetid
species = datastructure.get_species(inbredsetid)
speciesid = species[0]
print "speciesid: %s" % speciesid
# datafile
datafile = open(config.get('config', 'datafile'), 'r')
data = csv.reader(datafile, delimiter ="\t", quotechar='"')
strainnames = data.next()
print "strainnames: %s\n\t%s" % (len(strainnames), strainnames)
strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes")
print("strain: %s\n\t%s" % (len(strains), strains))
datafile.close()
def parse_genofile(params):
# genofile
with open(params['genofile']) as genofile:
meta_data = {}
print()
# parse genofile
for line in genofile:
line = line.strip()
if not line:
pass
elif line.startswith('#'):
pass
elif line.startswith('@'):
line = line.strip('@')
for item in line.split(';'):
kv = re.split(':|=', item)
meta_data[kv[0].strip()] = kv[1].strip()
elif line.lower().startswith("chr"):
print("geno file meta:")
for key, value in meta_data.iteritems():
print("\t{}: {}".format(key, value))
print("geno file head:\n\t{}\n".format(line))
strain_names = line.split()[4:]
strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid,
strain_names=strain_names,
updatestrainxref="yes")
else:
# geno file line
marker = Marker(line)
#
geno_id = check_or_insert_geno(params, marker)
if check_genoxref(params): #Check if this can go earlier
continue
insert_genodata(params)
insert_genoxref(params)
data_id += 1
def main(argv):
# config
config = utilities.get_config(argv[1])
print("config:")
for item in config.items('config'):
print(("\t%s" % (str(item))))
# var
inbredsetid = config.get('config', 'inbredsetid')
print(("inbredsetid: %s" % inbredsetid))
species = datastructure.get_species(inbredsetid)
speciesid = species[0]
print(("speciesid: %s" % speciesid))
dataid = datastructure.get_nextdataid_phenotype()
print(("next data id: %s" % dataid))
cursor, con = utilities.get_cursor()
# datafile
datafile = open(config.get('config', 'datafile'), 'r')
phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
phenotypedata_head = next(phenotypedata)
print(("phenotypedata head:\n\t%s" % phenotypedata_head))
strainnames = phenotypedata_head[1:]
strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes")
# metafile
metafile = open(config.get('config', 'metafile'), 'r')
phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
phenotypemeta_head = next(phenotypemeta)
print(("phenotypemeta head:\n\t%s" % phenotypemeta_head))
print()
# load
for metarow in phenotypemeta:
#
datarow_value = next(phenotypedata)
datarow_se = next(phenotypedata)
datarow_n = next(phenotypedata)
# Phenotype
sql = """
INSERT INTO Phenotype
SET
Phenotype.`Pre_publication_description`=%s,
Phenotype.`Post_publication_description`=%s,
Phenotype.`Original_description`=%s,
Phenotype.`Pre_publication_abbreviation`=%s,
Phenotype.`Post_publication_abbreviation`=%s,
Phenotype.`Lab_code`=%s,
Phenotype.`Submitter`=%s,
Phenotype.`Owner`=%s,
Phenotype.`Authorized_Users`=%s,
Phenotype.`Units`=%s
"""
cursor.execute(sql, (
utilities.to_db_string(metarow[1], None),
utilities.to_db_string(metarow[2], None),
utilities.to_db_string(metarow[3], None),
utilities.to_db_string(metarow[4], None),
utilities.to_db_string(metarow[5], None),
utilities.to_db_string(metarow[6], None),
utilities.to_db_string(metarow[7], None),
utilities.to_db_string(metarow[8], None),
utilities.to_db_string(metarow[9], ""),
utilities.to_db_string(metarow[18], ""),
))
rowcount = cursor.rowcount
phenotypeid = con.insert_id()
print(("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid)))
# Publication
publicationid = None # reset
pubmed_id = utilities.to_db_string(metarow[0], None)
if pubmed_id:
sql = """
SELECT Publication.`Id`
FROM Publication
WHERE Publication.`PubMed_ID`=%s
"""
cursor.execute(sql, (pubmed_id))
re = cursor.fetchone()
if re:
publicationid = re[0]
print(("get Publication record: %d" % publicationid))
if not publicationid:
sql = """
INSERT INTO Publication
SET
Publication.`PubMed_ID`=%s,
Publication.`Abstract`=%s,
Publication.`Authors`=%s,
Publication.`Title`=%s,
Publication.`Journal`=%s,
Publication.`Volume`=%s,
Publication.`Pages`=%s,
Publication.`Month`=%s,
Publication.`Year`=%s
"""
cursor.execute(sql, (
utilities.to_db_string(metarow[0], None),
utilities.to_db_string(metarow[12], None),
utilities.to_db_string(metarow[10], ""),
utilities.to_db_string(metarow[11], None),
utilities.to_db_string(metarow[13], None),
utilities.to_db_string(metarow[14], None),
utilities.to_db_string(metarow[15], None),
utilities.to_db_string(metarow[16], None),
utilities.to_db_string(metarow[17], ""),
))
rowcount = cursor.rowcount
publicationid = con.insert_id()
print(("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)))
# data
for index, strain in enumerate(strains):
#
strainid = strain[0]
value = utilities.to_db_float(datarow_value[index+1], None)
se = utilities.to_db_float(datarow_se[index+1], None)
n = utilities.to_db_int(datarow_n[index+1], None)
#
if value is not None:
sql = """
INSERT INTO PublishData
SET
PublishData.`Id`=%s,
PublishData.`StrainId`=%s,
PublishData.`value`=%s
"""
cursor.execute(sql, (dataid, strainid, value))
if se is not None:
sql = """
INSERT INTO PublishSE
SET
PublishSE.`DataId`=%s,
PublishSE.`StrainId`=%s,
PublishSE.`error`=%s
"""
cursor.execute(sql, (dataid, strainid, se))
if n is not None:
sql = """
INSERT INTO NStrain
SET
NStrain.`DataId`=%s,
NStrain.`StrainId`=%s,
NStrain.`count`=%s
"""
cursor.execute(sql, (dataid, strainid, n))
# PublishXRef
sql = """
INSERT INTO PublishXRef
SET
PublishXRef.`InbredSetId`=%s,
PublishXRef.`PhenotypeId`=%s,
PublishXRef.`PublicationId`=%s,
PublishXRef.`DataId`=%s,
PublishXRef.`comments`=%s
"""
cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, ""))
rowcount = cursor.rowcount
publishxrefid = con.insert_id()
print(("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid)))
# for loop next
dataid += 1
print()
# release
con.close()
def main(argv):
# config
config = utilities.get_config(argv[1])
print "config:"
for item in config.items('config'):
print "\t%s" % (str(item))
# var
inbredsetid = config.get('config', 'inbredsetid')
print "inbredsetid: %s" % inbredsetid
species = datastructure.get_species(inbredsetid)
speciesid = species[0]
print "speciesid: %s" % speciesid
dataid = datastructure.get_nextdataid_phenotype()
print "next data id: %s" % dataid
cursor, con = utilities.get_cursor()
# datafile
datafile = open(config.get('config', 'datafile'), 'r')
phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
phenotypedata_head = phenotypedata.next()
print("phenotypedata head [%d]:\n\t%s" % (len(phenotypedata_head), phenotypedata_head))
strainnames = phenotypedata_head[1:]
strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes")
# metafile
metafile = open(config.get('config', 'metafile'), 'r')
phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
phenotypemeta_head = phenotypemeta.next()
print("phenotypemeta head [%d]:\n\t%s" % (len(phenotypemeta_head), phenotypemeta_head))
print
# load
for metarow in phenotypemeta:
#
datarow_value = phenotypedata.next()
datarow_se = phenotypedata.next()
datarow_n = phenotypedata.next()
# Phenotype
sql = """
INSERT INTO Phenotype
SET
Phenotype.`Pre_publication_description`=%s,
Phenotype.`Post_publication_description`=%s,
Phenotype.`Original_description`=%s,
Phenotype.`Pre_publication_abbreviation`=%s,
Phenotype.`Post_publication_abbreviation`=%s,
Phenotype.`Lab_code`=%s,
Phenotype.`Submitter`=%s,
Phenotype.`Owner`=%s,
Phenotype.`Authorized_Users`=%s,
Phenotype.`Units`=%s
"""
cursor.execute(sql, (
utilities.to_db_string(metarow[1], None),
utilities.to_db_string(metarow[2], None),
utilities.to_db_string(metarow[3], None),
utilities.to_db_string(metarow[4], None),
utilities.to_db_string(metarow[5], None),
utilities.to_db_string(metarow[6], None),
utilities.to_db_string(metarow[7], None),
utilities.to_db_string(metarow[8], None),
utilities.to_db_string(metarow[9], ""),
utilities.to_db_string(metarow[18], ""),
))
rowcount = cursor.rowcount
phenotypeid = con.insert_id()
print "INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid)
# Publication
publicationid = None # reset
pubmed_id = utilities.to_db_string(metarow[0], None)
if pubmed_id:
sql = """
SELECT Publication.`Id`
FROM Publication
WHERE Publication.`PubMed_ID`=%s
"""
cursor.execute(sql, (pubmed_id))
re = cursor.fetchone()
if re:
publicationid = re[0]
print "get Publication record: %d" % publicationid
if not publicationid:
sql = """
INSERT INTO Publication
SET
Publication.`PubMed_ID`=%s,
Publication.`Abstract`=%s,
Publication.`Authors`=%s,
Publication.`Title`=%s,
Publication.`Journal`=%s,
Publication.`Volume`=%s,
Publication.`Pages`=%s,
Publication.`Month`=%s,
Publication.`Year`=%s
"""
cursor.execute(sql, (
utilities.to_db_string(metarow[0], None),
utilities.to_db_string(metarow[12], None),
utilities.to_db_string(metarow[10], ""),
utilities.to_db_string(metarow[11], None),
utilities.to_db_string(metarow[13], None),
utilities.to_db_string(metarow[14], None),
utilities.to_db_string(metarow[15], None),
utilities.to_db_string(metarow[16], None),
utilities.to_db_string(metarow[17], ""),
))
rowcount = cursor.rowcount
publicationid = con.insert_id()
print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)
# data
for index, strain in enumerate(strains):
#
strainid = strain[0]
value = utilities.to_db_float(datarow_value[index+1], None)
se = utilities.to_db_float(datarow_se[index+1], None)
n = utilities.to_db_int(datarow_n[index+1], None)
#
if value is not None:
sql = """
INSERT INTO PublishData
SET
PublishData.`Id`=%s,
PublishData.`StrainId`=%s,
PublishData.`value`=%s
"""
cursor.execute(sql, (dataid, strainid, value))
if se is not None:
sql = """
INSERT INTO PublishSE
SET
PublishSE.`DataId`=%s,
PublishSE.`StrainId`=%s,
PublishSE.`error`=%s
"""
cursor.execute(sql, (dataid, strainid, se))
if n is not None:
sql = """
INSERT INTO NStrain
SET
NStrain.`DataId`=%s,
NStrain.`StrainId`=%s,
NStrain.`count`=%s
"""
cursor.execute(sql, (dataid, strainid, n))
# PublishXRef
sql = """
INSERT INTO PublishXRef
SET
PublishXRef.`InbredSetId`=%s,
PublishXRef.`PhenotypeId`=%s,
PublishXRef.`PublicationId`=%s,
PublishXRef.`DataId`=%s,
PublishXRef.`comments`=%s
"""
cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, ""))
rowcount = cursor.rowcount
publishxrefid = con.insert_id()
print "INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid)
# for loop next
dataid += 1
print
# release
con.close()